mxtaltools.common.mol_classifier_utils
- mxtaltools.common.mol_classifier_utils.classifier_reporting(true_labels, true_defects, probs, class_names, ordered_class_names, wandb, epoch_type)[source]
- mxtaltools.common.mol_classifier_utils.convert_box_to_cell_vectors(box_params)[source]
LAMMPS periodic box style ITEM: BOX BOUNDS xy xz yz xlo_bound xhi_bound xy ylo_bound yhi_bound xz zlo_bound zhi_bound yz
a = xhi-xlo, 0, 0 b = xy, yhi-ylo, 0 c = xz, yz, zhi-zlo
xlo = xlo_bound - MIN(0, xy, xz, xy+xz) xhi = xhi_bound - MAX(0, xy, xz, xy+xz) ylo = ylo_bound - MIN(0, yz) yhi = yhi_bound - MAX(0, yz) zlo = zlo_bound zhi = zhi_bound
- mxtaltools.common.mol_classifier_utils.force_molecules_into_box(T_fc_list, cluster_coords, i, periodic)[source]
will fail on fragmented molecules or molecules otherwise wrapped
- mxtaltools.common.mol_classifier_utils.identify_surface_molecules(cluster_coords, cluster_targets, conv_cutoff, good_mols, mol_num_atoms, mol_radii)[source]
- mxtaltools.common.mol_classifier_utils.pare_cluster_radius(cluster_atoms, cluster_coords, cluster_targets, max_cluster_radius)[source]
- mxtaltools.common.mol_classifier_utils.pare_fragmented_molecules(cluster_atoms, cluster_coords, cluster_targets, pare_fragmented)[source]
Identify molecules which are fragmented, or split across a periodic boundary, and delete them.
Fragmented molecules are identified as having significanly larger molecular radii than normal. :param cluster_atoms: :param cluster_coords: :param cluster_targets: :param pare_fragmented:
Returns:
- mxtaltools.common.mol_classifier_utils.process_trajectory_results_dict(results_dict, loader, mol_num_atoms)[source]
- mxtaltools.common.mol_classifier_utils.record_step_results(results_dict, output, sample, data, latents, embeddings, step, config, index_offset=0)[source]